147 lines
5.9 KiB
C++
147 lines
5.9 KiB
C++
/**************************************************************************************/
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/* */
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/* Visualization Library */
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/* http://visualizationlibrary.org */
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/* */
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/* Copyright (c) 2005-2020, Michele Bosi */
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/* All rights reserved. */
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/* */
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/* Redistribution and use in source and binary forms, with or without modification, */
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/* are permitted provided that the following conditions are met: */
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/* */
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/* - Redistributions of source code must retain the above copyright notice, this */
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/* list of conditions and the following disclaimer. */
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/* */
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/* - Redistributions in binary form must reproduce the above copyright notice, this */
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/* list of conditions and the following disclaimer in the documentation and/or */
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/* other materials provided with the distribution. */
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/* */
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/* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND */
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/* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED */
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/* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE */
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/* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR */
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/* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES */
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/* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; */
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/* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON */
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/* ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT */
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/* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS */
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/* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */
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/* */
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/**************************************************************************************/
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#ifndef Atom_INCLUDE_ONCE
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#define Atom_INCLUDE_ONCE
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#include <vlCore/Object.hpp>
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#include <vlCore/Vector4.hpp>
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#include <vlMolecule/chem_database.hpp>
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#include <vector>
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namespace vl
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{
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/** The Atom class represents an atom to be used with the Molecule class.
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* \sa
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* - \ref pagGuideMolecule "Molecule Visualization Tutorial"
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* - Molecule
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* - Bond
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*
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* <img src="../pics/pagGuideMolecule.png">
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*/
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class Atom: public Object
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{
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VL_INSTRUMENT_CLASS(vl::Atom, Object)
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public:
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Atom()
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{
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VL_DEBUG_SET_OBJECT_NAME()
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mId = 0;
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mAtomType = AT_Unknown;
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mCoordinates = fvec3(0,0,0);
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mColor = fvec4(1.0f,1.0f,1.0f,1.0f);
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mRadius = 0.25f;
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mVisited = false;
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mVisible = true;
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mShowAtomName= false;
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/*mAtomName = nothing*/
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}
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Atom(const Atom& other): Object(other) { *this = other; }
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//! Assignment operator: does not assign the adjacent atoms
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Atom& operator=(const Atom& other)
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{
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mId = other.mId;
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mAtomType = other.mAtomType;
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mCoordinates = other.mCoordinates;
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mRadius = other.mRadius;
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mColor = other.mColor;
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mVisible = other.mVisible;
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mShowAtomName= other.mShowAtomName;
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// mAdjacentAtoms = other.mAdjacentAtoms; // do not copy
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// mVisited = other.mVisited; // do not copy
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mAtomName = other.mAtomName;
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return *this;
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}
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// Returns true if \p atom is adjacent to an Atom
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bool isAtomAdjacent(Atom* atom) const
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{
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for(unsigned i=0; i<adjacentAtoms().size(); ++i)
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if (adjacentAtoms()[i] == atom)
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return true;
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return false;
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}
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const std::vector< Atom* >& adjacentAtoms() const { return mAdjacentAtoms; }
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std::vector< Atom* >& adjacentAtoms() { return mAdjacentAtoms; }
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EAtomType atomType() const { return mAtomType; }
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void setAtomType(EAtomType type) { mAtomType = type; }
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unsigned int id() const { return mId; }
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void setId(unsigned int id) { mId = id; }
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const fvec3& coordinates() const { return mCoordinates; }
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void setCoordinates(const fvec3& coordinates) { mCoordinates = coordinates; }
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float radius() const { return mRadius; }
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void setRadius(float radius) { mRadius = radius; }
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void setVisited(bool visited) { mVisited = visited; }
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bool visited() const { return mVisited; }
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void setAtomName(const std::string& name) { mAtomName = name; }
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const std::string& atomName() const { return mAtomName; }
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const fvec4& color() const { return mColor; }
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void setColor(const fvec4& color) { mColor = color; }
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bool visible() const { return mVisible; }
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void setVisible(bool visible) { mVisible = visible; }
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//! Defines whether the atom name should be rendered or not. See also Molecule::setShowAtomNames().
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void setShowAtomName(bool show) { mShowAtomName = show; }
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//! Defines whether the atom name should be rendered or not. See also Molecule::setShowAtomNames().
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bool showAtomName() const { return mShowAtomName; }
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protected:
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fvec4 mColor;
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fvec3 mCoordinates;
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EAtomType mAtomType;
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float mRadius;
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std::vector< Atom* > mAdjacentAtoms;
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std::string mAtomName;
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unsigned int mId;
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// Aid to visit a molecule.
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bool mVisited;
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// Whether is visible or not
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bool mVisible;
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// Display atom name
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bool mShowAtomName;
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};
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}
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#endif
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